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Hi,
I filter variants from a WGS data with different databases like genomicSuperDups. However, many variants (more than 70%) get filtered by genomicSuperDups. As it is not normal, how is it possible to find out why so many variants get filtered? The problem is that annovar provides a list of dropped variants for different filters except genomicSuperDups. So there is no way to find out the variants that get filtered by this db.
another question is that if snp129 is more clean than snp137 in using snp137NonFlagged,snp137?
variants_reduction.pl myfile -protocol genomicSuperDups,1000g2012apr_all,snp137NonFlagged,snp137,dgv -buildver hg19 humandb/ -operation r,f,f,f,r -aaf_threshold .01 -remove
NOTICE: Processing operation=r protocol=genomicSuperDups
NOTICE: Running step 1 with system command <annotate_variation.pl -regionanno -dbtype genomicSuperDups -buildver hg19 -outfile myfile.step1 myfile.step0.varlist /humandb/>
NOTICE: Reading annotation database humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 2033 genetic variants in myfile.step0.varlist
NOTICE: Output files were written to myfile.step1.hg19_genomicSuperDups
NOTICE: After step 1, 61 variants are left in analysis.
I filter variants from a WGS data with different databases like genomicSuperDups. However, many variants (more than 70%) get filtered by genomicSuperDups. As it is not normal, how is it possible to find out why so many variants get filtered? The problem is that annovar provides a list of dropped variants for different filters except genomicSuperDups. So there is no way to find out the variants that get filtered by this db.
another question is that if snp129 is more clean than snp137 in using snp137NonFlagged,snp137?
variants_reduction.pl myfile -protocol genomicSuperDups,1000g2012apr_all,snp137NonFlagged,snp137,dgv -buildver hg19 humandb/ -operation r,f,f,f,r -aaf_threshold .01 -remove
NOTICE: Processing operation=r protocol=genomicSuperDups
NOTICE: Running step 1 with system command <annotate_variation.pl -regionanno -dbtype genomicSuperDups -buildver hg19 -outfile myfile.step1 myfile.step0.varlist /humandb/>
NOTICE: Reading annotation database humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 2033 genetic variants in myfile.step0.varlist
NOTICE: Output files were written to myfile.step1.hg19_genomicSuperDups
NOTICE: After step 1, 61 variants are left in analysis.